
<!DOCTYPE html>

<html>
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>pymatgen.analysis.prototypes &#8212; pymatgen 2020.7.3 documentation</title>
    <link rel="stylesheet" href="../../../_static/basic.css" type="text/css" />
    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
    <script id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
    <script src="../../../_static/jquery.js"></script>
    <script src="../../../_static/underscore.js"></script>
    <script src="../../../_static/doctools.js"></script>
    <script src="../../../_static/language_data.js"></script>
    <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
    <link rel="index" title="Index" href="../../../genindex.html" />
    <link rel="search" title="Search" href="../../../search.html" />
 
<script type="text/javascript">
  var _gaq = _gaq || [];
  _gaq.push(['_setAccount', 'UA-33990148-1']);
  _gaq.push(['_trackPageview']);
</script>

  </head><body>
    <div class="related" role="navigation" aria-label="related navigation">
      <h3>Navigation</h3>
      <ul>
        <li class="right" style="margin-right: 10px">
          <a href="../../../genindex.html" title="General Index"
             accesskey="I">index</a></li>
        <li class="right" >
          <a href="../../../py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
        <li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen 2020.7.3 documentation</a> &#187;</li>
          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &#187;</li>
          <li class="nav-item nav-item-2"><a href="../../pymatgen.html" accesskey="U">pymatgen</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.prototypes</a></li> 
      </ul>
    </div>  

    <div class="document">
      <div class="documentwrapper">
          <div class="body" role="main">
            
  <h1>Source code for pymatgen.analysis.prototypes</h1><div class="highlight"><pre>
<span></span><span class="c1"># coding: utf-8</span>
<span class="c1"># Copyright (c) Pymatgen Development Team.</span>
<span class="c1"># Distributed under the terms of the MIT License.</span>

<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">This module is intended to match crystal structures against known crystallographic &quot;prototype&quot;</span>
<span class="sd">structures.</span>

<span class="sd">In this module, the AflowPrototypeMatcher uses the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.</span>
<span class="sd">If using this particular class, please cite their publication appropriately:</span>

<span class="sd">Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
<span class="sd">The AFLOW library of crystallographic prototypes: part 1.</span>
<span class="sd">Computational Materials Science, 136, S1-S828.</span>
<span class="sd">https://doi.org/10.1016/j.commatsci.2017.01.017</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">os</span>

<span class="kn">from</span> <span class="nn">monty.serialization</span> <span class="kn">import</span> <span class="n">loadfn</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.structure_matcher</span> <span class="kn">import</span> <span class="n">StructureMatcher</span>

<span class="n">module_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span>
<span class="n">AFLOW_PROTOTYPE_LIBRARY</span> <span class="o">=</span> <span class="n">loadfn</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)),</span>
                                              <span class="s2">&quot;aflow_prototypes.json&quot;</span><span class="p">))</span>


<div class="viewcode-block" id="AflowPrototypeMatcher"><a class="viewcode-back" href="../../../pymatgen.analysis.prototypes.html#pymatgen.analysis.prototypes.AflowPrototypeMatcher">[docs]</a><span class="k">class</span> <span class="nc">AflowPrototypeMatcher</span><span class="p">:</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    This class will match structures to their crystal prototypes, and will</span>
<span class="sd">    attempt to group species together to match structures derived from</span>
<span class="sd">    prototypes (e.g. an A_xB_1-x_C from a binary prototype), and will</span>
<span class="sd">    give these the names the &quot;-like&quot; suffix.</span>

<span class="sd">    This class uses data from the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.</span>
<span class="sd">    If using this class, please cite their publication appropriately:</span>

<span class="sd">    Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
<span class="sd">    The AFLOW library of crystallographic prototypes: part 1.</span>
<span class="sd">    Computational Materials Science, 136, S1-S828.</span>
<span class="sd">    https://doi.org/10.1016/j.commatsci.2017.01.017</span>
<span class="sd">    &quot;&quot;&quot;</span>

    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">initial_ltol</span><span class="o">=</span><span class="mf">0.2</span><span class="p">,</span> <span class="n">initial_stol</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">initial_angle_tol</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Tolerances as defined in StructureMatcher. Tolerances will be</span>
<span class="sd">        gradually decreased until only a single match is found (if possible).</span>

<span class="sd">        Args:</span>
<span class="sd">            initial_ltol: fractional length tolerance</span>
<span class="sd">            initial_stol: site tolerance</span>
<span class="sd">            initial_angle_tol: angle tolerance</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">initial_ltol</span> <span class="o">=</span> <span class="n">initial_ltol</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">initial_stol</span> <span class="o">=</span> <span class="n">initial_stol</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">initial_angle_tol</span> <span class="o">=</span> <span class="n">initial_angle_tol</span>

    <span class="nd">@staticmethod</span>
    <span class="k">def</span> <span class="nf">_match_prototype</span><span class="p">(</span><span class="n">structure_matcher</span><span class="p">,</span> <span class="n">structure</span><span class="p">):</span>
        <span class="n">tags</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">AFLOW_PROTOTYPE_LIBRARY</span><span class="p">:</span>
            <span class="n">p</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;snl&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">structure</span>
            <span class="n">match</span> <span class="o">=</span> <span class="n">structure_matcher</span><span class="o">.</span><span class="n">fit_anonymous</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">structure</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
                <span class="n">tags</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
        <span class="k">return</span> <span class="n">tags</span>

    <span class="k">def</span> <span class="nf">_match_single_prototype</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">):</span>
        <span class="n">sm</span> <span class="o">=</span> <span class="n">StructureMatcher</span><span class="p">(</span><span class="n">ltol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">initial_ltol</span><span class="p">,</span>
                              <span class="n">stol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">initial_stol</span><span class="p">,</span>
                              <span class="n">angle_tol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">initial_angle_tol</span><span class="p">)</span>
        <span class="n">tags</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_prototype</span><span class="p">(</span><span class="n">sm</span><span class="p">,</span> <span class="n">structure</span><span class="p">)</span>
        <span class="k">while</span> <span class="nb">len</span><span class="p">(</span><span class="n">tags</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
            <span class="n">sm</span><span class="o">.</span><span class="n">ltol</span> <span class="o">*=</span> <span class="mf">0.8</span>
            <span class="n">sm</span><span class="o">.</span><span class="n">stol</span> <span class="o">*=</span> <span class="mf">0.8</span>
            <span class="n">sm</span><span class="o">.</span><span class="n">angle_tol</span> <span class="o">*=</span> <span class="mf">0.8</span>
            <span class="n">tags</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_prototype</span><span class="p">(</span><span class="n">sm</span><span class="p">,</span> <span class="n">structure</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">sm</span><span class="o">.</span><span class="n">ltol</span> <span class="o">&lt;</span> <span class="mf">0.01</span><span class="p">:</span>
                <span class="k">break</span>
        <span class="k">return</span> <span class="n">tags</span>

<div class="viewcode-block" id="AflowPrototypeMatcher.get_prototypes"><a class="viewcode-back" href="../../../pymatgen.analysis.prototypes.html#pymatgen.analysis.prototypes.AflowPrototypeMatcher.get_prototypes">[docs]</a>    <span class="k">def</span> <span class="nf">get_prototypes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Get prototype(s) structures for a given</span>
<span class="sd">        input structure. If you use this method in</span>
<span class="sd">        your work, please cite the appropriate</span>
<span class="sd">        AFLOW publication:</span>

<span class="sd">        Mehl, M. J., Hicks, D., Toher, C., Levy, O.,</span>
<span class="sd">        Hanson, R. M., Hart, G., &amp; Curtarolo, S. (2017).</span>
<span class="sd">        The AFLOW library of crystallographic prototypes: part 1.</span>
<span class="sd">        Computational Materials Science, 136, S1-S828.</span>
<span class="sd">        https://doi.org/10.1016/j.commatsci.2017.01.017</span>

<span class="sd">        Args:</span>
<span class="sd">            structure: structure to match</span>

<span class="sd">        Returns (list): A list of dicts with keys</span>
<span class="sd">        &#39;snl&#39; for the matched prototype and &#39;tags&#39;,</span>
<span class="sd">        a dict of tags (&#39;mineral&#39;, &#39;strukturbericht&#39;</span>
<span class="sd">        and &#39;aflow&#39;) of that prototype. This should</span>
<span class="sd">        be a list containing just a single entry,</span>
<span class="sd">        but it is possible a material can match</span>
<span class="sd">        multiple prototypes.</span>
<span class="sd">        &quot;&quot;&quot;</span>

        <span class="n">tags</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_single_prototype</span><span class="p">(</span><span class="n">structure</span><span class="p">)</span>

        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tags</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
            <span class="k">return</span> <span class="kc">None</span>
        <span class="k">else</span><span class="p">:</span>
            <span class="k">return</span> <span class="n">tags</span></div></div>
</pre></div>

            <div class="clearer"></div>
          </div>
      </div>
      <div class="clearer"></div>
    </div>
    <div class="related" role="navigation" aria-label="related navigation">
      <h3>Navigation</h3>
      <ul>
        <li class="right" style="margin-right: 10px">
          <a href="../../../genindex.html" title="General Index"
             >index</a></li>
        <li class="right" >
          <a href="../../../py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
        <li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen 2020.7.3 documentation</a> &#187;</li>
          <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &#187;</li>
          <li class="nav-item nav-item-2"><a href="../../pymatgen.html" >pymatgen</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.prototypes</a></li> 
      </ul>
    </div>

    <div class="footer" role="contentinfo">
        &#169; Copyright 2011, Pymatgen Development Team.
      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.1.2.
    </div>
<div class="footer">This page uses <a href="http://analytics.google.com/">
Google Analytics</a> to collect statistics. You can disable it by blocking
the JavaScript coming from www.google-analytics.com.
<script type="text/javascript">
  (function() {
    var ga = document.createElement('script');
    ga.src = ('https:' == document.location.protocol ?
              'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
    ga.setAttribute('async', 'true');
    document.documentElement.firstChild.appendChild(ga);
  })();
</script>
</div>

  </body>
</html>